The human gut microbiota makes important functional contributions to the host's metabolism and physiological traits, but remains largely unknown due to its complexity. To generate DNA materials of the microbial species from the human microbiota suitable for genomic sequencing, we propose to design, construct and test droplet based microfluidic devices for the co-cultivation and analysis of various subsets of the total gut microbiota. We will pursue two aims: Specific Aim 1: Design and construct microfluidic components for cell encapsulation, co-cultivation, and genetic characterization. Specific Aim 2: Test the devices with a synthetic model system and gut microbial samples from gnotobiotic animals. PUBLIC HEALTH RELEVANCE: Microbial communities in the gastrointestinal tract have been found to make functional contributions to the host's metabolism and physiological traits, such as digestion and immunity. To facilitate the cultivation of these gut microbes and to eventually elucidate the underlying microbe-microbe and host-microbe interactions, we propose to design and build a prototype microfluidic platform to compartmentalize, co-cultivate and analyze various subsets of the total gut microbiota.